R Notebook

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Try executing this chunk by clicking the Run button within the chunk or by placing your cursor inside it and pressing Ctrl+Shift+Enter. # Cellchat

source("./tianfengRwrappers.R")

library(CellChat)

ds2 <- readRDS("ds2.rds")
CA_dataset2 <- readRDS("CA_dataset2.rds")
# saveRDS(CA_dataset2,"CA_dataset2.rds")
umapplot(CA_dataset2)

Warning: Using `as.character()` on a quosure is deprecated as of rlang 0.3.0.
Please use `as_label()` or `as_name()` instead.
This warning is displayed once per session.

f("DLX5",EC_SMC)
umapplot(EC_SMC)

saveRDS(EC_SMC,"EC_SMC.rds")

CellChat

配体-受体+辅因子

computeAveExpr(cor, features = c("BMP2","BMP4","BMP6","BMPR1B","BMPR1A","BMPR2","ACVR2A"), type =  "truncatedMean", trim = 0.05)

                3        EC0         EC1         EC2 Fibroblast Fibromyocyte    Pericyte        SMC1       SMC2
BMP2   0.03150669 0.02623810 0.003702709 0.202131802 0.00000000   0.00000000 0.028212306 0.000000000 0.00000000
BMP4   0.00000000 0.02969807 0.064427142 0.535072542 0.14289603   0.05976591 0.000000000 0.008078115 0.02235959
BMP6   0.33885091 0.00000000 0.000000000 0.430656995 0.00000000   0.00000000 0.000000000 0.000000000 0.00000000
BMPR1B 0.00000000 0.00000000 0.000000000 0.000000000 0.08194540   0.00000000 0.000000000 0.008751292 0.07602259
BMPR1A 0.00000000 0.00000000 0.000000000 0.006539124 0.05175499   0.03366126 0.009241962 0.057668768 0.02832214
BMPR2  0.30466733 0.28211628 0.328085107 0.880202371 0.11521646   0.13015395 0.078799890 0.157702091 0.11248721
ACVR2A 0.00000000 0.00000000 0.000000000 0.000000000 0.01848392   0.00000000 0.000000000 0.000000000 0.00000000

write.csv(df.net,"./datatable/EC_SMC_cellchat_res.csv", row.names = F)

cellchat可视化

cor <- readRDS("EC_SMC_cellchat.rds")

Loading required package: CellChat
Loading required package: igraph

Attaching package: ‘igraph’

The following object is masked from ‘package:circlize’:

    degree

The following object is masked from ‘package:Mfuzz’:

    membership

The following object is masked from ‘package:DynDoc’:

    path

The following objects are masked from ‘package:BiocGenerics’:

    normalize, path, union

The following object is masked from ‘package:plotly’:

    groups

The following object is masked from ‘package:clusterProfiler’:

    simplify

The following object is masked from ‘package:tidyr’:

    crossing

The following objects are masked from ‘package:dplyr’:

    as_data_frame, groups, union

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

Registered S3 methods overwritten by 'registry':
  method               from 
  print.registry_field proxy
  print.registry_entry proxy

#指定pathway
pathways.show <- c("BMP") 

netVisual_aggregate(cor, signaling = pathways.show, layout = "circle")

# netVisual_aggregate(cor, signaling = pathways.show, layout = "chord")

# Heatmap
netVisual_heatmap(cor, signaling = pathways.show, color.heatmap = c("#f1f1f1", "#ff2121"))

Do heatmap based on a single object 

netVisual_bubble(cor, sources.use = 4, targets.use = c(5:9), pairLR.use = LR_show, remove.isolate = F) #EC2 target

Comparing communications on a single object 

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